Evaluation of the portability of computable phenotypes with natural language processing in the eMERGE network.

The electronic Medical Records and Genomics (eMERGE) Network assessed the feasibility of deploying portable phenotype rule-based algorithms with natural language processing (NLP) components added to improve performance of existing algorithms using electronic health records (EHRs). Based on scientific merit and predicted difficulty, eMERGE selected six existing phenotypes to enhance with NLP. We assessed performance, portability, and ease of use. We summarized lessons learned by: (1) challenges; (2) best practices to address challenges based on existing evidence and/or eMERGE experience; and (3) opportunities for future research. Adding NLP resulted in improved, or the same, precision and/or recall for all but one algorithm. Portability, phenotyping workflow/process, and technology were major themes. With NLP, development and validation took longer. Besides portability of NLP technology and algorithm replicability, factors to ensure success include privacy protection, technical infrastructure setup, intellectual property agreement, and efficient communication. Workflow improvements can improve communication and reduce implementation time. NLP performance varied mainly due to clinical document heterogeneity; therefore, we suggest using semi-structured notes, comprehensive documentation, and customization options. NLP portability is possible with improved phenotype algorithm performance, but careful planning and architecture of the algorithms is essential to support local customizations.

A new approach to categorization of radiologic inflammation in chronic rhinosinusitis.

Chronic rhinosinusitis (CRS) is a prevalent condition. Clinical diagnosis requires subjective evidence (i.e. symptoms) and objective evidence of inflammation (e.g. sinus computed tomography [CT]). Few studies have assessed differences in common CT scoring approaches for CRS, the Lund-Mackay (LM) system and its modified version (mLM); none in a general population sample. The aims of this study were to answer the following: (1) Is mLM superior to LM? (2) Should nasal cavity opacification be included in scoring? (3) How should location-specific scores be utilized? (4) If location-specific scores are summed, what should be the cutoff? (5) Are associations of opacification with symptoms observed when using different measurement approaches? We scored sinus CTs using LM and mLM from 526 subjects selected from a larger CRS study. Exploratory factor analysis (EFA) assessed similarity of mLM and LM. Latent class analysis (LCA) identified subgroups of sinus opacification patterns. Factors associated with group membership and relations with nasal and sinus symptoms (NSS) guided clinical relevance. EFA suggested no differences between LM and mLM, or after addition of nasal cavity opacification. LCA identified three opacification groups: no/mild, localized, and diffuse. Males were 2.7x more likely to have diffuse opacification than females, as were those with asthma or hay fever. A LM cutoff of 3 had similar performance to the currently used 4. Diffuse opacification was associated with nasal blockage and smell loss. Differing patterns of opacification may be clinically relevant, improving measurement of objective evidence in studies of CRS and sinus diseases.

Workplace Indirect Cost Impacts of Nasal and Sinus Symptoms and Related Conditions.

OBJECTIVE: Evaluate associations of nasal and sinus and related symptoms, as well as selected health conditions which produce those symptoms, with total lost productive time (LPT) at work in the past 2 weeks. METHODS: We used a cross-sectional analysis of 2402 currently working subjects. Self-reported physician diagnoses, condition statuses measured with standardized instruments, and symptom-based factor scores from an exploratory factor analysis were used in survey weighted log-binomial regression. RESULTS: Pain and pressure, nasal blockage and discharge, and asthma and constitutional symptom factor scores as well as self-reported allergic rhinitis were associated with higher total LPT. Individuals who met operationalized criteria for multiple health conditions, especially chronic rhinosinusitis, had the greatest total LPT. CONCLUSIONS: Better management of these symptoms, and awareness of how they impact an individual's ability to perform job-functions in the workplace, could improve overall productivity.

Clinical burden of asynchrony in patients with asthma when using metered-dose inhalers for control.

Background: Asynchrony, or lack of coordination between inhalation and actuation when using a pressurized metered-dose inhaler (MDI), could theoretically impact the delivery of inhaled medications and treatment efficacy. Objective: To assess the real-world association between asynchrony and clinical outcomes among patients with asthma who receive controller therapy delivered by MDIs. Methods: A cohort of patients was assembled via electronic health records. The patients were aged ≥12 years, with one or more documentations of an asthma diagnosis, no diagnosis of chronic obstructive pulmonary disease, and two or more prescriptions for an inhalation aerosol corticosteroid alone or with long-acting beta-2-agonist delivered via MDI. Their inhaler technique, demonstrated by using a placebo MDI, was evaluated at a clinic visit by study nurses who used a standardized 10-step checklist. Asynchrony was defined as any gap in timing between inhalation and actuation. Clinical outcomes were assessed via electronic health records during the 6 months before the clinic visit and were compared between patients with and patients without asynchrony by using multivariable regression analyses adjusted for age, gender, asthma severity proxy, and baseline comorbidities. Results: Of the total 254 eligible patients, mean age of 49.3 years, 90 males (35.4%), 32 (12.6%) had asynchrony. Patients with asynchrony had higher odds of an asthma exacerbation (adjusted odds ratio, 2.99; p = 0.009), and lower odds of risk domain asthma control (adjusted odds ratio, 0.41; p = 0.04) compared with patients without asynchrony. Conclusion: This study provided real-world evidence that asynchrony in MDI use among patients with asthma who were treated with controller MDIs was associated with clinical burden in terms of asthma exacerbations and control.

Identifying Asthma Exacerbation-Related Emergency Department Visit Using Electronic Medical Record and Claims Data.

BACKGROUND: Asthma exacerbation leading to emergency department (ED) visit is prevalent, an indicator of poor control of asthma, and is a potentially preventable clinical outcome. OBJECTIVE: We propose to utilize multiple data elements available in electronic medical records (EMRs) and claims database to create separate algorithms with high validity for clinical and research purposes to identify asthma exacerbation-related ED visit among the general population. METHODS: We performed a retrospective study with inclusion criteria of patients aged 4 to 40 years, a visit to Geisinger ED from January 1, 2006, to October 28, 2013, with asthma on their problem list. Different electronic data elements including chief complaints, vitals, season, smoking, medication use, and discharge diagnoses were obtained to create the algorithm. A stratified random sample was generated to select the charts for review. Chart review was performed to classify patients with asthma-related ED visit, that is, the gold standard. Two reviewers performed the chart review and validation was done on a small subset. RESULTS: There were 966 eligible ED visits in the EMR sample and 731 in the claims sample. Agreement between reviewers was 95.45% and kappa statistic was 0.91. Mean age of the EMR sample was 22 years, and mostly white (93%). Multiple models conventionally used in studies were evaluated and the final model chosen included principal diagnosis, bronchodilator, and steroid use for both algorithms, chief complaints for EMR, and secondary diagnosis for claims. Area under the curve was 0.93 (95% confidence interval: 0.91-0.94) and 0.94 (0.93-0.96), respectively, for EMR and claims data, with positive predictive value of > 94%. The algorithms are visually presented using nomograms. CONCLUSION: We were able to develop two separate algorithms for EMR and claims to identify asthma exacerbation-related ED visit with excellent diagnostic ability and varying discrimination threshold for clinical and research purposes.

Longitudinal Evaluation of Chronic Rhinosinusitis Symptoms in a Population-Based Sample.

BACKGROUND: Chronic rhinosinusitis (CRS) is a prevalent and disabling condition of the nose and sinuses. The natural history of CRS symptoms in a general population sample has not been previously studied. OBJECTIVE: In a general population-based sample from Pennsylvania, we used 2 questionnaires mailed 6 months apart to estimate the prevalence of, and identify predictors for, stability or change in symptoms over time. METHODS: We mailed the baseline and 6-month follow-up questionnaires to 23,700 primary care patients and 7,801 baseline responders, respectively. We categorized nasal and sinus symptoms using European Position Paper on Rhinosinusitis (EPOS) epidemiologic criteria. We defined 6 symptom groups over time on the basis of the presence of CRS symptoms at baseline and follow-up. We performed multivariable survey logistic regression controlling for confounding variables comparing persistent versus nonpersistent, recurrent versus stable past, and incident versus never. RESULTS: There were 4,966 responders at follow-up: 558 had persistent symptoms, 190 recurrent symptoms, and 83 new symptoms meeting EPOS criteria for CRS. The prevalence of persistent symptoms was 4.8% (95% CI, 3.8-5.8), whereas the annual cumulative incidence of new symptoms was 1.9% and of recurrent symptoms was 3.2%. More severe symptoms at baseline were associated with persistence, whereas minor symptoms, allergies, and multiple treatments were associated with the development of new symptoms. CONCLUSIONS: Less than half with nasal and sinus symptoms meeting CRS EPOS criteria in our general, regional population had symptom persistence over time, with symptom profiles at baseline and age of onset being strongly associated with stability of symptoms.

Identification of Four Novel Loci in Asthma in European American and African American Populations.

RATIONALE: Despite significant advances in knowledge of the genetic architecture of asthma, specific contributors to the variability in the burden between populations remain uncovered. OBJECTIVES: To identify additional genetic susceptibility factors of asthma in European American and African American populations. METHODS: A phenotyping algorithm mining electronic medical records was developed and validated to recruit cases with asthma and control subjects from the Electronic Medical Records and Genomics network. Genome-wide association analyses were performed in pediatric and adult asthma cases and control subjects with European American and African American ancestry followed by metaanalysis. Nominally significant results were reanalyzed conditioning on allergy status. MEASUREMENTS AND MAIN RESULTS: The validation of the algorithm yielded an average of 95.8% positive predictive values for both cases and control subjects. The algorithm accrued 21,644 subjects (65.83% European American and 34.17% African American). We identified four novel population-specific associations with asthma after metaanalyses: loci 6p21.31, 9p21.2, and 10q21.3 in the European American population, and the PTGES gene in African Americans. TEK at 9p21.2, which encodes TIE2, has been shown to be involved in remodeling the airway wall in asthma, and the association remained significant after conditioning by allergy. PTGES, which encodes the prostaglandin E synthase, has also been linked to asthma, where deficient prostaglandin E2 synthesis has been associated with airway remodeling. CONCLUSIONS: This study adds to understanding of the genetic architecture of asthma in European Americans and African Americans and reinforces the need to study populations of diverse ethnic backgrounds to identify shared and unique genetic predictors of asthma.

Penetrance of Hemochromatosis in HFE Genotypes Resulting in p.Cys282Tyr and p.[Cys282Tyr];[His63Asp] in the eMERGE Network.

Hereditary hemochromatosis (HH) is a common autosomal-recessive disorder associated with pathogenic HFE variants, most commonly those resulting in p.Cys282Tyr and p.His63Asp. Recommendations on returning incidental findings of HFE variants in individuals undergoing genome-scale sequencing should be informed by penetrance estimates of HH in unselected samples. We used the eMERGE Network, a multicenter cohort with genotype data linked to electronic medical records, to estimate the diagnostic rate and clinical penetrance of HH in 98 individuals homozygous for the variant coding for HFE p.Cys282Tyr and 397 compound heterozygotes with variants resulting in p.[His63Asp];[Cys282Tyr]. The diagnostic rate of HH in males was 24.4% for p.Cys282Tyr homozygotes and 3.5% for compound heterozygotes (p < 0.001); in females, it was 14.0% for p.Cys282Tyr homozygotes and 2.3% for compound heterozygotes (p < 0.001). Only males showed differences across genotypes in transferrin saturation levels (100% of homozygotes versus 37.5% of compound heterozygotes with transferrin saturation > 50%; p = 0.003), serum ferritin levels (77.8% versus 33.3% with serum ferritin > 300 ng/ml; p = 0.006), and diabetes (44.7% versus 28.0%; p = 0.03). No differences were found in the prevalence of heart disease, arthritis, or liver disease, except for the rate of liver biopsy (10.9% versus 1.8% [p = 0.013] in males; 9.1% versus 2% [p = 0.035] in females). Given the higher rate of HH diagnosis than in prior studies, the high penetrance of iron overload, and the frequency of at-risk genotypes, in addition to other suggested actionable adult-onset genetic conditions, opportunistic screening should be considered for p.[Cys282Tyr];[Cys282Tyr] individuals with existing genomic data.

Occupational and environmental risk factors for chronic rhinosinusitis: a systematic review.

BACKGROUND: Chronic rhinosinusitis (CRS) is a prevalent and disabling paranasal sinus disease, with a likely multifactorial etiology potentially including hazardous occupational and environmental exposures. We completed a systematic review of the occupational and environmental literature to evaluate the quality of evidence of the role that hazardous exposures might play in CRS. METHODS: We searched PubMed for studies of CRS and following exposure categories: occupation, employment, work, industry, air pollution, agriculture, farming, environment, chemicals, roadways, disaster, and traffic. We abstracted information from the final set of articles across 6 primary domains: study design; population; exposures evaluated; exposure assessment; CRS definition; and results. RESULTS: We identified 41 articles from 1080 manuscripts: 37 occupational risk papers, 1 environmental risk paper, and 3 papers studying both categories of exposures. None of the 41 studies used a CRS definition consistent with current diagnostic guidelines. Exposure assessment was generally dependent on self-report or binary measurements of exposure based on industry of employment. Only grain, dairy, and swine operations among farmers were evaluated by more than 1 study using a common approach to defining CRS, but employment in these settings was not consistently associated with CRS. The multiple other exposures did not meet quality standards for reporting associations or were not evaluated by more than 1 study. CONCLUSION: The current state of the literature allows us to make very few conclusions about the role of hazardous occupational or environmental exposures in CRS, leaving a critical knowledge gap regarding potentially modifiable risk factors for disease onset and progression.